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CHEM 223: Mass Spectrometry

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Chem 223 Course Outline
Chem 223 - Lectures

Fall 2007

NOTES:

  • Lecture list shown below is still in progress and will be updated as we go along.
  • Lecture notes for each lecture can be obtained from the lecture notes download page.
  • Some lectures may be finished in less than one lecture period.  Some lectures (indicated by a double entry below) may require two lecture periods to cover the material
Lecture Topic Reading Assignment Go to Topics in Reading
List Below
0
  • Introduction to course & mass spectrometry
Dass Chap 1 Intro articles
1
  • Mass spectrometry - the physics of ions in space
    • definition of mass spectrometry and a mass spectrometer
    • formation & acceleration of ions -- basic equations
    • dispersion of ions in a magnetic field -- basic equations
    • elementary focusing of beams
   
2
  • Double focusing
    • electric fields and electrostatic focussing
    • combination of electrostatic and magnetic fields
    • mass resolution
de Hoffmann Chap 2.4-2.6
Watson Chap 4: pp 68-73
McCloskey Chap 2: pp 37-47, Chap 6, & Appendix 1 		Ion optics
3
  • Isotopes and ion abundances
    • exact mass calculations
    • calculating theoretical isotope distributions
    • calculating isotopomer distributions
de Hoffmann Chap 5.2-5.3
Watson Chap 7: pp 151-158
McCloskey Appendix 4 		 
4
  • Time of flight (TOF)
de Hoffmann Chap 2.3 TOF
5
  • Quadrupole rod mass analyzer
Watson Chap 4: pp 73-105
de Hoffmann Chap 2.1-2.2 		Quads & ion traps
6
  • Detectors
    • Faraday cup
    • Electron multipliers & conversion dynodes
    • Multichannel plates
Watson Chap 13
McCloskey Chap 3 		 
7
  • Electron impact (EI) ionization
    • ion source design
    • interpreting EI fragmentation spectra
Watson Chap 7: pp 139-151
de Hoffmann Chap 1.1 & Chap 6
McCloskey Chap 1: pp 1-10 		 
8
  • Chemical ionization (CI)
    • mechanism
    • source design
    • negative chemical ionization (NCI)
Watson Chap 8
de Hoffmann Chap 1.2
McCloskey Chap 1: pp 10-20 		CI
9
  • Vacuum systems
    • Vacuum pumps
    • Vacuum gauges
Watson Chap 19
McCloskey Chap 3 		Vacuum
10
  • Equations of vacuum: "the arithmetic of emptiness"
  • Simple sample introduction
    • gas & liquid "leaks", solid probes
Watson Chap 6 Vacuum
11
  • GCMS interfaces & rudimentary LCMS interfaces
Watson Chap 16 & 17
de Hoffmann Chap 1.7
McCloskey Chap 5 		GC & LC interfaces
12
  • LCMS atmospheric pressure interfaces:
    • electrospray ionization (ESI)
    • deconvolution of multiply charged envelopes
    • atmospheric pressure CI (APCI)
Watson Chap 11
de Hoffmann Chap 1.8-1.9 		ESI
APCI
13
  • Surface ionization
    • fast atom bombardment (FAB)
    • matrix assisted laser desorption ionization (MALDI)
Watson Chap 9 & Chap 10
de Hoffmann Chap 1.3-1.6
McCloskey Chap 1: pp 21-37, Chap 8, Chap 9, & Appendix 3 		FAB
MALDI
14
  • Ion trap mass analyzer
Watson Chap 4: pp 73-105
de Hoffmann Chap 2.1-2.2 		Quads & ion traps
15
  • Fourier transform (FT) ion cyclotron resonance (ICR) MS
de Hoffmann Chap 2.5 FTMS
16
  • Tandem mass spectrometry - MS/MS
    • Metastable ions & double focusing BE systems
    • post source decay (PSD)
    • CID
      • quadrupole triple-sector instruments
      • hybrids (QTOF)
      • ion trap & MSn
      • FTMS
      • TOF & TOF-TOF
Watson Chap 5
de Hoffmann Chap 2.3.4 & 3
McCloskey Chap 6 & Chap 10 		MS/MS
17
  • The Orbitrap MS — illustration of the journal club presentation
  Orbitrap
18a
18b
  • Proteins, peptide sequencing & proteomics
    • MALDI/TOF
    • ESI
    • database searching
de Hoffmann Chap 7.2
McCloskey Chap 12 		Proteomics
19
  • Quantitative proteomics
  Proteomics
20
  • Isotope ratio mass spectrometry
McCloskey Chap 3  

  • Reading List:

    • Almost all of the papers are obtainable on-line as a PDF through the UVM Library or can be downloaded by clicking here or by clicking on the link in the menu to the left for "PDF files of MS articles".
    • References for which there is no PDF file available are shown in green -- generally these references are of lesser importance.
    • Books obtainable from the library are shown in maroon.
  • Reading keyed to lectures:
    • See syllabus for list of books and reference materials.
  • Introductory articles:
    • Price: Standard definitions of terms relating to mass spectrometry: A report from the Committee on Measurements and Standards of the American Society for Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2(4): 336-348, 1991.
    • Tutorial on Mass Spectrometry from the ASMS
    • WD Lehmann: Pictograms for experimental parameters in mass spectrometry. J. Am. Soc. Mass Spectrom. 8: 756-759, 1997.
  • Ion optics:
    • H Wollnik, Ion optics in mass spectrometers. J. Mass Spectrom.34: 991-1006, 1999. Although dry to read, this tutorial contains a variety of references for further reading.
  • Vacuum:
    • Saul Dushman, Scientific Foundations of Vacuum Technique, 2nd ed., New York, Wiley, 1962. Cook Library QC166 .D85 1962. Chapter 2: arithmetic of emptiness equations
    • D.P. Shoemaker, C.W. Garland,& J.W. Nibler, Chap 27: Vacuum techniques, Experiments in Physical Chemistry , 5th ed, McGraw-Hill, NY, 1989, pp 677-714.
  • Chemical ionization:
    • A. G. Harrison, Chemical Ionization Mass Spectrometry, 2nd ed., CRC Press, 1992. Cook Library QD96.M3 H37 1992. Chapters 2 & 4.
  • GC & LC interfaces:
    • J Abian: The coupling of gas and liquid chromatography with mass spectrometry. J. Mass Spectrom. 34: 157-168, 1999.
    • AP Bruins, TR Covey & JD Henion: Ion spray interface for combined liquid chromatography/atmospheric pressure ionization mass spectrometry. Anal. Chem. 59: 2642-2646, 1987.
  • ESI:
    • E Gelpi: Interfaces for coupled liquid-phase separation/mass spectrometry techniques. An update on recent developments. J. Mass Spectrom. 37: 241-253, 2002.
    • RB Cole: Some tenets pertaining to electrospray ionization mass spectrometry. J. Mass Spectrom. 35: 763-772, 2000.
    • JF Mora, GJ Van Berkel, CG Enke, RB Cole, M Martinez-Sanchez & JB Fenn: Electrochemical processes in electrospray ionization mass spectrometry. J. Mass Spectrom. 35: 939-952, 2000.
    • Cole, R.B.: Electrospray Ionization Mass Spectrometry, John Wiley & Sons, NY, 1997. In the Cook Library QP519.9.M3 E44 1997.
    • SJ Gaskell: Electrospray: Principles and practice. J. Mass Spectrom. 32: 677-688, 1997.
    • JB Fenn, J Rosell & CK Meng: In electrospray ionization, how much pull does an ion need to escape its droplet prison? J. Am. Soc. Mass Spectrom. 8: 1147-1157, 1997.
    • JF Banks, Jr. & CM Whitehouse: Electrospray ionization mass spectrometry. Methods Enzymol. 270: 486-519, 1996.
    • MT Davis: Micro electrospray interface design and method selection for tandem MS analyses of complex peptide mixtures. 1997.
    • M Mann, CK Meng & JB Fenn: Interpreting mass spectra of multiply charged ions. Anal. Chem. 61: 1702-1708, 1989.
    • MH Amad, NB Cech, GS Jackson & CG Enke: Importance of gas-phase proton affinities in determining the electrospray ionization response for analytes and solvents. J. Mass Spectrom. 35: 784-789, 2000.
    • P Kebarle: A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry. J. Mass Spectrom. 35: 804-817, 2000.
    • T Blades, MG Ikonomou & P Kebarle: Mechanism of electrospray mass spectrometry. Electrospray as an electrolysis cell. Anal. Chem. 63: 2109-2114, 1991.
    • P Kebarle & L Tang: From ions in solution to ions in the gas phase. Anal. Chem. 65: 972A-986A, 1993.
    • L Tang & P Kebarle: Dependence of ion intensity in electrospray mass spectrometry on the concentration of the analytes in the electrosprayed solution. Anal. Chem. 65: 3654-3668, 1993.
  • APCI:
    • EC Horning, MG Horning, DI Carroll, I Dzidic & RN Stillwell: New picogram detection system based on a mass spectrometer with an external ionization source at atmospheric pressure. Anal. Chem. 45: 936-943, 1973.
    • EC Horning, DI Carroll, I Dzidic, KD Haegele, S Lin, CU Oertli & RN Stillwell: Development and use of analytical systems based on mass spectrometry. Clin. Chem. 23: 13-21, 1977.
    • AM Lovett, NM Reid, JA Buckley, JB French & DM Cameron: Real-time analysis of breath using an atmospheric pressure ionization mass spectrometer. Biomed. Mass Spectrom. 6: 91-97, 1979.
    • D Smith & P Spanel: The novel selected-ion flow tube approach to trace gas analysis of air and breath. Rapid Commun. Mass Spectrom. 10: 1183-1198, 1996.
    • E Brewer & J Henion: Atmospheric pressure ionization LC/MS/MS techniques for drug disposition studies. J. Pharm. Sci. 87: 395-402, 1998.
  • Quadrupoles & ion traps:
    • MB Denton & PE Miller: The quadrupole mass filter: Basic operating concepts. J. Chem. Educ. 63: 617-622, 1986.
    • JJ Leary & RL Schmidt: Quadrupole mass spectrometers: An intuitive look at the math. J. Chem. Educ. 73: 1142-1145, 1996.
    • RE March: An introduction to quadrupole ion trap mass spectrometry. J.Mass Spectrom. 32: 351-369, 1997.
    • KR Jonscher & JR Yates, III: The quadrupole ion trap mass spectrometer--A small solution to a big challenge. Anal.Biochem. 244: 1-15, 1997.
    • G Stafford, Jr.: Ion trap mass spectrometry: A personal perspective. J. Am. Soc. Mass Spectrom. 13: 589-596, 2002.
    • NV Konenkov, M Sudakov & DJ Douglas: Matrix methods for the calculation of stability diagrams in quadrupole mass spectrometry. J. Am. Soc. Mass Spectrom. 13: 597-613, 2002.
    • KR Jonscher & JR Yates, III: The whys and wherefores of quadrupole ion trap mass spectrometry. 1996.
    • JC Schwartz & I Jardine: Quadrupole ion trap mass spectrometry. Methods Enzymol. 270: 552-586, 1996.
  • FTMS or FT-ICR
    • AG Marshall & PB Grosshans: Fourier transform ion cyclotron resonance mass spectrometry: The teenage years. Anal.Chem. 63: 215A-229A, 1991.
    • IJ Amster: Fourier transform mass spectrometry. J.Mass Spectrom. 31: 1325-1337, 1996.
    • AG Marshall, CL Hendrickson & GS Jackson: Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17: 1-35, 1998.
  • Orbitrap
    • A Makarov: Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal. Chem. 72: 1156-1162, 2000.
    • M Hardman & AA Makarov: Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal. Chem. 75: 1699-1705, 2003.
    • Q Hu, RJ Noll, H Li, A Makarov, M Hardman & CR Graham: The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 40: 430-443, 2005.
    • JV Olsen, LM de Godoy, G Li, B Macek, P Mortensen, R Pesch, A Makarov, O Lange, S Horning & M Mann: Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 4: 2010-2021, 2005.
    • Q Hu, AA Makarov, RG Cooks & RJ Noll: Resonant ac dipolar excitation for ion motion control in the Orbitrap mass analyzer. J. Phys. Chem. A 110: 2682-2689, 2006.
    • A Makarov, E Denisov, A Kholomeev, W Balschun, O Lange, K Strupat & S Horning: Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78: 2113-2120, 2006.
    • A Makarov, E Denisov, O Lange & S Horning: Dynamic range of mass accuracy in LTQ Orbitrap hybrid mass spectrometer. J. Am. Soc. Mass Spectrom. 17: 977-982, 2006.
    • M Scigelova & A Makarov: Orbitrap mass analyzer - overview and applications in proteomics. Proteomics 6: 16-21, 2006.
  • TOF:
    • Time-of-flight mass spectrometry: Instrumentation and applications in biological research. Robert J. Cotter ed. American Chemical Society, 1997. Dana: QC 454 M3 C847t 1997 -- lots of material taken from this book for the TOF lecture.
    • RJ Cotter: The new time-of-flight mass spectrometry. Anal. Chem. 71: 445A-451A, 1999.
    • M Guilhaus: Principles and instrumentation in time-of-flight mass spectrometry: Physical and instrumental concepts. J. Mass Spectrom. 30: 1519-1532, 1995.
    • M Vestal & P Juhasz: Resolution and mass accuracy in matrix-assisted laser desorption ionization time-of-flight. J.Am.Soc.Mass Spectrom. 9: 892-911, 1998.
  • MALDI:
    • JJ Lennon: Matrix assisted laser desorption ionization time-of-flight mass spectrometry. 1997.
    • M Karas, M Glückmann & J Schäfer: Ionization in matrix-assisted laser desorption/ionization: Singly charged molecular ions are the lucky survivors. J. Mass Spectrom. 35: 1-12, 2000.
    • M Glückmann & M Karas: The initial ion velocity and its dependence upon matrix, analyte, and preparation method in ultraviolet matrix-assisted laser desorption/ionization. J. Mass Spectrom. 34: 467-477, 1999.
    • RS Brown & JJ Lennon: Mass resolution improvement by incorporation of pulsed ion extraction in a matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometer. Anal.Chem. 67: 1998-2003, 1995.
    • DH Russell & RD Emondson: High-resolution mass spectrometry and accurate mass meaurements with emphasis on the characterization of peptides and proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectometry. J. Mass Spectrom. 32: 263-276, 1997.
  • FAB:
    • M Barber, RS Bordoll, GJ Elliott, RD Sedgwick & AN Tyler: Fast atom bombardment mass spectrometry. Anal. Chem. 54: 645A-657A, 1982.
  • MS/MS:
    • E de Hoffmann: Tandem mass spectrometry: A primer. J. Mass Spectrom. 31: 129-137, 1996.
    • B Spengler: Post-source decay analysis in matrix-assisted laser desorption/ionization mass spectrometry of biomolecules. J. Mass Spectrom. 32: 1019-1036, 1997.
    • KF Medzihradszky, JM Campbell, MA Baldwin, AM Falick, P Juhasz, ML Vestal & AL Burlingame: The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 72: 552-558, 2000.
    • IV Chernushevich, AV Loboda & BA Thomson: An introduction to quadrupole-time-of-flight mass spectrometry. J. Mass Spectrom. 36: 849-865, 2001.
  • Proteomics:
    • JR Yates, III: Mass spectrometry and the age of the proteome. J. Mass Spectrom. 33: 1-19, 1998.
    • J Peng & SP Gygi: Proteomics: The move to mixtures.  J. Mass Spectrom. 36: 1083-1091, 2001.
    • MJ MacCoss & DE Matthews: Quantitative mass spectrometry for proteomics: Teaching a new dog old tricks. Anal. Chem. 77: 294A-302A, 2005.
  • Inductively coupled plasma (ICP) MS (topic not covered):
    • D Stuewer & N Jakubowski: Elemental analysis by inductively coupled plasma mass spectrometry with sector field instruments: A progress report. J. Mass Spectrom. 33: 579-590, 1998.

Last modified November 16 2007 11:07 AM

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